Curriculum

The week leading up to the first fall semester is an Orientation Week for incoming students. Prior to matriculation and in advance of Orientation Week, the CMBS program interacts with trainees to help them get acquainted with the graduate school and overall aspects related to graduate student life, including ensuring housing arrangements have been made. Also prior to matriculation, the Systems Biology program director meets virtually with the incoming students to discuss possible mentors for their first laboratory rotation. During orientation week, the program director then meets in-person with the students to discuss the basics of the program, including course requirements, laboratory rotations, qualifying examinations, student seminars and any other requirements. The program director is responsible for most of the direct advising during the first year regarding coursework, rotations, and any other issues that arise. There are formal meetings with first-year students three times a year, once during Orientation Week and at the end of each semester.

The Office of Graduate Affairs (OGA) holds a series of orientation events to acclimate the students to the campus and the city. In addition, the OGA hosts a number of lectures/mini-courses on topics related to ethical and policy issues that may arise during the conduct of research, including experimental design, research and data integrity, laboratory safety, student conduct, mentoring, and fostering a safe and inclusive work environment. There will also be a Faculty Poster Session during Orientation Week to give students a chance to interact with faculty and learn about research opportunities.

Laboratory rotations are designed to assist students in identifying the most beneficial research and mentoring environment in which to complete their graduate studies. They also give the students first-hand experience in a variety of techniques and approaches to biological problems. Our students are required to do at least two lab rotations but generally do three rotations during their first year. Rotations occur from September-December, January-March, and April-June.

The Faculty Poster Session and individual meetings with the program director during Orientation Week provides new students with specific guidance and opportunities for detailed discussions about rotations and other matters. Even more notable is the Department of Systems Biology Annual Retreat each fall during which students will meet not only our faculty but also our graduate students, postdoctoral fellows, and other scientists.

Reflecting the interdisciplinary nature of the discipline, Systems Biology PhD students are currently required to take six core courses, including two systems biology courses, two biology-themed courses, and two statistical or computational courses.  

• First year fall semester: Core Course 1 and 2
• First year spring semester: Core Course 3 and 4
• Second year fall semester: Core Course 5 and 6
• Second year spring semester: CMBS/DSB Student Presentation Practicum
• Third year fall semester: Small Group Discussion - Responsible Conduct of Research

During the second semester of the second year, DSB students prepare for their qualifying examination. This examination is used as a formal evaluation of the student’s potential as a candidate for the Ph.D. degree. It is designed to assess the student’s ability to develop a sophisticated, in-depth understanding of their thesis project and it also serves as a tool for identifying deficiencies in the students’ background that could be remedied by further coursework or additional reading. Students present a written research proposal on their thesis topic. The proposal is written in the format of an NIH F31 fellowship and consists of a description of the background and significance of the topic, the specific aims of the proposed research, and the research methods to address the aims. Preliminary data (if available) can also be presented, but since the examination is given shortly after the trainee begins the project, it is not required.

The student along with their thesis advisor proposes three committee members who will serve as examiners. The program director reviews the proposed committee members and if approved, one will serve as committee chair. After the student submits the proposal, an oral examination is scheduled. During the oral examination, the student presents the proposal in the style of a ‘chalk talk’ during which the committee poses questions related to the written proposal and topics from coursework.

In the spring or summer of the second year, the student have the first meeting with their thesis committees. The thesis committee is typically the same as the qualifying examination committee, although occasionally one of the members might be replaced, especially if the student’s research is going in a different direction. These committees provide scientific expertise related to the students’ projects and monitor thesis research. For the first meeting, the students should present a short, written report that contains the specific aims of their proposal and present the progress they have made since the qualifying examination to the committee. The committee recommends the priorities for the order in which the work will proceed, as well as the chosen design of experiments. It is possible that the committee may recommend changes to experimental design or priorities. The committee also decides when to have the next meeting, which can be either in 3, 6 or 9 months after the meeting. For these later meetings, the students prepare a 1–2 page report outlining their progress on the previous aims and present their timetable for finishing their thesis work. The committee can and should recommend improvements to experimental strategies and fallback plans for difficult or risky experiments.

Either in the spring or the summer of the second year, students choose their thesis committees with the help of their research advisor. These committees will provide scientific expertise related to the students’ projects and they monitor the progress that the student makes during their thesis research.  DSB students are required to have three faculty members in addition to their PhD advisor on their thesis committee, and at least one of these three faculty members must be on the DSB faculty. (In the event that the student’s advisor is not a DSB faculty member, the student must have at least two faculty members.)

Students must follow the Graduate School of Arts & Sciences dissertation formatting guidelines. It is recommended that the contents are presented as follows:

Chapter 1: Introduction – this should be a scholarly synthesis of the necessary background that is the foundation for the thesis work.

Chapter 2: Materials and methods – this should be a compilation of all methods for the entire thesis.

Chapters 3, 4, etc.: Results – each chapter typically correspond to an individual manuscript comprised of a short introduction (1-3 pages), the results, figures, and a short summary discussion. Consult the formatting guidelines.

Final chapter: Conclusions including future directions.

After the thesis committee gives its approval for the student to write up the thesis, the defense is scheduled. The final thesis committee consists of the mentor, the three thesis committee members and one additional examiner.  If the additional examiner is from outside the university, they have to be approved by the Program and the Dissertation office as a competent examiner. The thesis should be submitted to the committee two weeks before the scheduled defense. A public presentation is given immediately before the closed defense. At the time of the closed defense, the student may be asked to make additional revisions. On rare occasions, the student may be required to do additional experimental work, extensive revisions of thesis, and/or a second dissertation defense. Students are required to submit a first author paper before their defense.

Systems biology track students participate in the CMBS Seminar series in both the fall and spring semesters of their first and second years. For Systems Biology students, the fall Faculty Seminar Series is held every Monday evening (5p-6p) and the spring Series is held every other Tuesday (4p-5:15p). In addition, the CMBS program offers a bi-weekly fall Faculty Seminar Series every other Tuesday evening at which other Faculty affiliated with the CMBS program present; Systems Biology students are encouraged (but not required) to attend the fall Tuesday series. The overall goals of the Seminar courses are to:

•    Learn about systems biology, broadly defined

•    Learn about research in the Systems Biology Department

•    Learn about scientists as individuals

•    Learn how to give a research presentation to an educated – but non-expert – audience

•    Learn how to give useful feedback

A monthly seminar series, organized jointly by DSB students and postdocs provides graduate students and postdoctoral fellows to present their research to the department followed by a social gathering. This is an excellent career- and community-building activity.

DSB Program Retreat: A critical component of the DSB training program is the annual Systems Biology retreat. The retreat is held off-campus typically in October. For 2023, the retreat was hosted at Woodloch Pines in Pennsylvania, and time was included in the schedule to take advantage of the many outdoor activities available, and graduate students create a team-building activity of their choice. The retreat includes shared meals, talks by faculty, postdocs, and students, and research poster presentations by students. Fellowships are awarded to posters by faculty evaluators. The retreat offers our students an excellent opportunity to interact with faculty, postdocs, and their graduate program peers.

CMBS Program Retreat: An important special feature of the CMBS Program is the program retreat. The retreat is held off-campus biennially, and on campus the other year. The next off campus retreat will be held in September 2025 and is organized by trainees of the CMBS Program and two junior faculty members. The retreat includes talks and research poster presentations by students. Thus, the retreat gives our students an excellent chance to present their work in front of a friendly, but diverse audience.